[Bio-Linux] Bio-Linux 2.1 Upgrades, Bio-Linux installs and Bio-Linux news

[Dr Dan Swan]

Dear Bio-Linux users,

As some of you may be aware we recently committed Bio-Linux 2.1.  This
release has now passed the testing phase and we are looking to roll out
upgrades across the board soon.

For those interested in the changes that have been made you can view
changes on the public Bio-Linux changelog:

http://envgen.nox.ac.uk/envgen/software/archives/000309.html

There are a number of significant bug-fixes as well as new software.  A
lot of the changes described are as a result of user feedback over the
last few months, and we would like to take this opportunity to thank
everyone who has flagged an issue with Bio-Linux they have come across
and reported to us.  We do encourage any feedback on the Bio-Linux
system and it contributes greatly to future development of the project.

The upgrade process is relatively straightforward and does not require
re-installation of the machine.  You can view the instructions on
updating your machine here:

http://envgen.nox.ac.uk/envgen/software/archives/000360.html

Upgrades for those who have not added additional software packages or
modules is especially straightforward.  For people who have heavily
customised their systems the upgrade will require some discussion with
the EGTDC about the updateclient.local.exclude file.

If you are the systems administrator of a Bio-Linux machine please start
thinking about the customisations and additional software packages you
have installed on the machine.  Obviously these should be included in
the log book we hope you keep with your machines detailing all the
changes you make to the system.

We will be contacting people individually soon in order to proceed with
the upgrades.  If you would like to become an early adopter of the
upgrades then please write to helpdesk at envgen.nox.ac.uk with a list of
the machines you want to update, and we will take it from there. 
Updates will be rolled out from next week.

Bio-Linux 2.1 is likely to be the last major release in the 2.X series
barring minor bug-fixes.  The EGTDC is now committed to the development
of the first Bio-Linux 3.0 release which is scheduled for a December
2003 release.  Again, we invite suggestions for what you would like to
see in this release as it will be a significant step forward in
functionality, look and feel.  The changelog will detail development of
Bio-Linux 3.0 as it happens.

We would also like to take this opportunity to apologise for the delay
in rolling out installs to those (few) remaining awardees.  Due to the
recent attack of Blaster worms (and variants) JANET and UKERNA and many
individual institutions have decided to disallow "ping" traffic on their
networks.  Unfortunately the Bio-Linux install process relies on this
working, and we are currently in discussion with the developers of our
distribution system (SystemImager) on a resolution for this.  We expect
this to be remedied by the end of next week and will resume installs
then.  This does not affect upgrades to the system however. 

Due to popular demand we are also re-running the Basic Bio-Linux course
in the new practical based format on November 25th.  If people came on
the Bio-Linux course prior to June 2003 they will not have had the
opportunity to work in the GRID room on Bio-Linux workstations at CEH
Oxford.  If you would like to attend, or would like colleagues to attend
then please email the helpdesk.  The new course includes basic Linux
usage, a bioinformatics practical and a hands on demonstration and
practical with GeneSpring.

regards,

Dan and the EGTDC team.

-- 
Dr Dan Swan - Bio-Linux Developer
EGTDC, CEH, Mansfield Road, Oxford, OX1 3SR
Tel: 01865 281 975 Fax: 01865 281 696
http://envgen.nox.ac.uk/ | dswan at ceh.ac.uk